Citation and License

BMC Genomics 2012, 13:162
doi:10.1186/1471-2164-13-162

Published: 3 May 2012

Abstract

Background

The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic
species scattered across taxonomic groups. Experimental detection of nitrogen fixation
in microbes requires species-specific conditions, making it difficult to obtain a
comprehensive census of this trait. The recent and rapid increase in the availability
of microbial genome sequences affords novel opportunities to re-examine the occurrence
and distribution of nitrogen fixation genes. The current practice for computational
prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes.

Results

Based on a careful comparison of the repertoire of nitrogen fixation genes in known
diazotroph species we propose a new criterion for computational prediction of nitrogen
fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and
NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced
genomes and identified 149 diazotrophic species, including 82 known diazotrophs and
67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation
in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we
predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla
had not hitherto been known to contain species capable of nitrogen fixation. Our analyses
also identified protein sequences that are similar to nitrogenase in organisms that
do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins
lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests
their potential for performing other, as yet unidentified, metabolic functions.

Conclusions

Our predictions expand the known phylogenetic diversity of nitrogen fixation, and
suggest that this trait may be much more common in nature than it is currently thought.
The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential
new roles for anciently duplicated and divergent members of this group of enzymes.